library(tidyverse)
Registered S3 methods overwritten by 'dbplyr':
method from
print.tbl_lazy
print.tbl_sql
-- Attaching packages ---------------------------------------------------------------------- tidyverse 1.3.1 --
√ ggplot2 3.3.5 √ purrr 0.3.4
√ tibble 3.1.6 √ dplyr 1.0.8
√ tidyr 1.2.0 √ stringr 1.4.0
√ readr 2.1.2 √ forcats 0.5.1
-- Conflicts ------------------------------------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
library(tuneR)
library(devtools)
Loading required package: usethis
library(ggplot2)
library(tsfeatures)
Registered S3 method overwritten by 'quantmod':
method from
as.zoo.data.frame zoo
library(class)
library(cvTools)
Loading required package: lattice
Loading required package: robustbase
library(randomForest)
randomForest 4.7-1
Type rfNews() to see new features/changes/bug fixes.
Attaching package: ‘randomForest’
The following object is masked from ‘package:dplyr’:
combine
The following object is masked from ‘package:ggplot2’:
margin
library(GEOquery)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object is masked from ‘package:randomForest’:
combine
The following object is masked from ‘package:tuneR’:
normalize
The following objects are masked from ‘package:dplyr’:
combine, intersect, setdiff, union
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated,
eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
see 'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:robustbase’:
rowMedians
The following object is masked from ‘package:tuneR’:
channel
Registered S3 method overwritten by 'data.table':
method from
print.data.table
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
library(R.utils)
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.
Attaching package: ‘R.oo’
The following object is masked from ‘package:R.methodsS3’:
throw
The following objects are masked from ‘package:devtools’:
check, unload
The following objects are masked from ‘package:methods’:
getClasses, getMethods
The following objects are masked from ‘package:base’:
attach, detach, load, save
R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help.
Attaching package: ‘R.utils’
The following object is masked from ‘package:GEOquery’:
gunzip
The following object is masked from ‘package:tidyr’:
extract
The following object is masked from ‘package:utils’:
timestamp
The following objects are masked from ‘package:base’:
cat, commandArgs, getOption, inherits, isOpen, nullfile, parse, warnings
library(reshape2)
Attaching package: ‘reshape2’
The following object is masked from ‘package:tidyr’:
smiths
library(limma)
Attaching package: ‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
library(dplyr)
library(e1071)
library(DT)
Registered S3 methods overwritten by 'htmltools':
method from
print.html tools:rstudio
print.shiny.tag tools:rstudio
print.shiny.tag.list tools:rstudio
Registered S3 method overwritten by 'htmlwidgets':
method from
print.htmlwidget tools:rstudio
library(viridis)
Loading required package: viridisLite
library(plotly)
Attaching package: ‘plotly’
The following object is masked from ‘package:ggplot2’:
last_plot
The following object is masked from ‘package:stats’:
filter
The following object is masked from ‘package:graphics’:
layout
library(scales)
Attaching package: ‘scales’
The following object is masked from ‘package:viridis’:
viridis_pal
The following object is masked from ‘package:purrr’:
discard
The following object is masked from ‘package:readr’:
col_factor
gse36059 = getGEO("GSE36059")[[1]]
Found 1 file(s)
GSE36059_series_matrix.txt.gz
|--------------------------------------------------|
|==================================================|
gse48581 = getGEO("GSE48581")[[1]]
Found 1 file(s)
GSE48581_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz
gse129166 = getGEO("GSE129166")[[1]]
Found 1 file(s)
GSE129166_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz
gse15296 = getGEO("GSE15296")[[1]]
Found 1 file(s)
GSE15296_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\LIAM~1.MCC\AppData\Local\Temp\RtmpAdkIfN/GPL570.soft.gz
gse36074_f = fData(gse36059)
gse36074_f
gse36074_f = fData(gse48581)
gse36074_f
gse129166_f = fData(gse129166)
gse129166_f
gse15296_f = fData(gse15296)
gse15296_f
gse36074_p = pData(gse36059)
gse36074_p
gse48581_p = pData(gse48581)
gse48581_p
gse129166_p = pData(gse129166)
gse129166_p
gse15296_p = pData(gse15296)
gse15296_p
data.frame(ifelse(gse36074_p$characteristics_ch1) == "diagnosis: non-rejecting", 0, 1)
Main outcomes are non-rejecting, TCMR (acute T-cell–mediated rejection), ABMR (anti-donor antibody-mediated rejection), and MIXED. Also has nephrectomy.
gse36074_ex = data.frame(t(exprs(gse36059)))
gse36074_ex